Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
  • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
  • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
  • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
  • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
  • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
  • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
  • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
  • C07K14/32—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Bacillus (G)

Definitions

• sequence listing that is contained in the file named "seqlisting_55486A_PCT.txt", which is 500832 bytes (measured in operating system MS-Windows), created on August 07, 2009, is filed herewith by electronic submission and incorporated herein by reference in its entirety.
• transgenic plant cells in seeds and plants with improved stress tolerance and methods of making and using such cells, seeds and plants.
• This invention provides novel proteins derived from bacterial cold shock proteins, which upon expression in transgenic plants provide the plants with enhanced stress tolerance.
• This invention also provides recombinant DNA constructs for expression of such polypeptides.
• a recombinant DNA construct comprises a promoter that functions in plants operably linked to nucleotides encoding a protein having a sequence of any one of SEQ ID NO: 15 through SEQ ID NO:33 or SEQ ID NO:53 through SEQ ID NO:704, wherein said recombinant DNA construct is stably integrated into a chromosome in a transgenic plant cell.
• the polypeptides provide plants with improved yield as compared to control crop plants when the plants are grown under abiotic stress conditions, including high salt, heat, drought or water deficit and cold temperatures.
• Abiotic stress tolerant plants express the variant bacterial cold shock proteins of this invention, and include crop plants that are improved in at least one trait selected from heat tolerance, salt tolerance, drought tolerance, and survival after cold shock.
• the modified bacterial cold shock proteins also provide crop plants having comparable or improved yield as compared to control crop plants when grown in non-stress conditions, including conditions of moderate temperatures and sufficient water.
• Crop plants of particular interest in the present invention include corn, soybean, cotton, canola, alfalfa, wheat, rice, switchgrass, sugarcane, and sugar beet.
• This invention also provides transgenic plant cells, propagules, including seeds, and crops having the novel recombinant DNA of this invention.
• a plant chromosome having stably integrated DNA for expression of a variant bacterial cold shock protein is provided.
• Transgenic pollen grains comprising a hap Io id derivative of a plant cell containing a plant chromosomal DNA segment of this invention are also provided.
• Another aspect of this invention is anti-counterfeit milled seed having, as an indication of origin, a plant cell with said chromosomal DNA segment of this invention.
• the present invention is also directed to methods of plant and seed production.
• One method provides for the production of transgenic plants having enhanced abiotic stress tolerance by introducing (by transformation or intra gressing) recombinant DNA for expression of a variant bacterial cold shock protein into plant cells to provide transgenic plant cells, regenerating a transgenic plant from one or more of said transgenic plant cells, and screening a population of transgenic plants to select a transgenic plant expressing a variant bacterial cold shock protein and having enhanced abiotic stress tolerance.
• Another method of this invention provides for the manufacture of non- natural, transgenic seed or propagules that can be used to produce a crop of transgenic plants with enhanced abiotic stress tolerance resulting from expression of a variant bacterial cold shock protein from a plant chromosomal DNA segment of this invention.
• Such a method comprises screening a population of plants having such plant chromosomal DNA segment for said enhanced abiotic stress tolerance, selecting from said population one or more plants that exhibit enhanced yield as compared to the yield for control plants under abiotic stress conditions, verifying that said plant chromosomal DNA segment is stably integrated in said selected plants, and collecting seed or a regenerative propagule from a selected plant.
• Another method provides for the production of inbred corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a stably- integrated, chromosomal DNA segment of this invention comprising recombinant DNA for expression of a variant bacterial cold shock protein, introgressing the chromosomal DNA segment from said acquired hybrid corn seed into a second corn line by allowing pollen grains comprising a haploid derivative with said chromosomal DNA segment to pollinate said second corn line to produce crossed seeds, producing a population of plants from crossed seeds (where a fraction of the seeds produced from said pollination is homozygous for the chromosomal DNA segment, a fraction is hemizygous, and a fraction does not have the chromosomal DNA segment), selecting corn plants which are homozygous and hemizygous for said chromosomal DNA segment by treating with an herbicide, collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants, and backcross
• Yet another aspect of this invention provides a method of growing a corn, cotton, soybean, sugarcane, switchgrass, rice, wheat, alfalfa, or canola crop without irrigation water comprising planting seed having plant cells with a plant chromosomal DNA segment of this invention, where the seeds are produced from plants that are selected for enhanced water deficit stress tolerance.
• Recombinant DNAs comprising a promoter that functions in plants operably linked to a polynucleotide encoding a protein, wherein the protein is a chimeric bacterial cold shock protein wherein at least one Reg 1, Reg 2, Reg 3, Reg 4, or Reg 5 amino acid region of a first bacterial cold shock protein is substituted with at least one corresponding Reg 1, Reg 2, Reg 3, Reg 4, or Reg 5 amino acid region of at least one second bacterial cold shock protein are provided.
• the first bacterial cold shock protein is selected from the group consisting of CspB, CspC, CspD, CspG, Cspl, and Csp2.
• the first bacterial cold shock protein is a CspB protein that comprises a CspB L2V protein.
• a CspB L2V protein can comprise the protein of SEQ ID NO: 1.
• the second bacterial cold shock protein can be selected from the group consisting of a Thermotoga maritima cold shock protein, a Thertnoanaerobacter tengcongensis cold shock protein, an Escherichia coli cold shock protein, and an Agrobacterium tumefaciens cold shock protein.
• the second bacterial cold shock protein can also be selected from the group consisting of a Thermotoga maritima Cspl cold shock protein, a Thermo anaerobacter tengcongensis Cspl cold shock protein, an Escherichia coli CspC cold shock protein, an Escherichia coli CspD cold shock protein, an Escherichia coli CspG cold shock protein, and an Agrobacterium tumefaciens Csp2 cold shock protein.
• the recombinant DNA encodes a chimeric bacterial cold shock protein that comprises a protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 16 through SEQ ID NO:23, SEQ ID NO: 313 through SEQ ID NO:426, and SEQ ID NO:427.
• recombinant DNAs comprising a promoter that functions in plants operably linked to a polynucleotide encoding a protein, wherein the protein is a variant of a Bacillus subtilis cspB protein having one or more amino acid substitutions in an amino acid position corresponding to amino acids Fl 5, F 17, F27, H29, or F30 of Bacillus subtilis cspB of SEQ ID NO:1.
• the recombinant DNA encodes a protein that comprises a protein with an amino acid sequence selected from the group consisting of SEQ ID NO:53 through SEQ ID NO:57, SEQ ID NO:458 through SEQ ID NO:577, and SEQ ID NO:578.
• recombinant DNAs comprising a promoter that functions in plants operably linked to a polynucleotide encoding a protein, wherein the protein is a variant of a Bacillus subtilis cspB protein having one or more amino acid substitutions in an amino acid position corresponding to amino acids S31 and T40 of Bacillus subtilis cspB of SEQ ID NO:1.
• the recombinant DNAs encodes a protein that comprises a protein with an amino acid sequence selected from the group consisting of SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:428 through SEQ ID NO:456, and SEQ ID NO:457.
• recombinant DNAs comprising a promoter that functions in plants operably linked to a polynucleotide encoding a protein, wherein the protein is a variant of a Bacillus subtilis cspB protein having at least two amino acid residues N and N+2 replaced with alanine residues, wherein N corresponds to any one of amino acids 2 - 65 of SEQ ID NO: 1.
• the protein encoded by the recombinant DNA comprises a protein with an amino acid sequence selected from the group consisting of SEQ ID NO:270 through SEQ ID NO:311, and SEQ ID NO:312.
• recombinant DNAs comprising a promoter that functions in plants operably linked to a polynucleotide encoding a protein, wherein said protein is a variant of a Bacillus subtilis cspB protein comprising a mutation in a DOTl, DOT2, DOT3, DOT4, DOT5a, DOT5b, or DOT6 region of a Bacillus subtilis CspB protein, wherein said DOTl, DOT2, DOT3, DOT4, DOT5a, DOT5b, or DOT6 region are as provided in Figure 2.
• the protein encoded by the recombinant DNA comprises a protein with an amino acid sequence selected from the group consisting of SEQ ID NO:15, SEQ ID NO:24 through SEQ ID NO:31, SEQ ID NO:58 through SEQ ID NO:269, SEQ ID NO:579 through SEQ ID NO:703, and SEQ ID NO:704.
• any of the aforementioned recombinant DNAs wherein the promoter is selected from the group consisting of inducible promoters, constitutive promoters, temporal-regulated promoters, developmentally-regulated promoters, tissue-preferred promoters, cold enhanced promoters, cold-specific promoters, stress enhanced promoters, stress specific promoters, drought inducible promoters, water deficit inducible promoters, and tissue-specific promoters.
• the cell is selected from the group consisting of a bacterial cell, a yeast cell, an isolated mammalian cell, and a plant cell.
• the cell is a plant cell, wherein the plant cell is in a transgenic plant, wherein any of the aforementioned recombinant DNAs is stably integrated into a chromosome of said transgenic plant cell and wherein the recombinant DNA confers abiotic stress-tolerance.
• the plant cell is in a transgenic plant, the plant is selected from the group consisting of soybean, corn, canola, rice, cotton, barley, oats, alfalfa, sugarcane, turf grass, cotton, and wheat.
• non-natural transgenic plant comprising a plurality of plant cells comprising the aforementioned recombinant DNA molecules
• a plant propagule of the transgenic plants comprising a plurality of plant cells comprising the aforementioned recombinant DNA molecules.
• the plant propagule is a seed.
• Also provided are methods for obtaining an abiotic-stress resistant plant comprising planting of a seed of the transgenic plants comprising a plurality of plant cells comprising the aforementioned recombinant DNA molecules.
• methods of producing non-natural transgenic plant seed comprising the steps of: a) screening a population of plants for enhanced abiotic stress tolerance and the presence of any of the aforementioned recombinant DNAs, wherein individual plants in the population exhibit said abiotic stress tolerance at a level less than, essentially the same as, or greater than the level that said abiotic stress tolerance is exhibited in control plants that do not contain said recombinant DNA; b) selecting from said population one or more plants that exhibit said abiotic stress tolerance trait at a level greater than the level that said trait is exhibited in control plants; and c) collecting seed from selected plants from step b.
• the enhanced abiotic stress tolerance is to an abiotic stress is selected from the group consisting of heat tolerance, salt
• proteins encoded by the polynucleotide that is operably linked to the promoter of any of the aforementioned the recombinant DNAs.
• this protein is in a plant cell. In still other embodiments, this protein is in a processed plant product.
• processed plant products comprising a detectable amount of the polynucleotide that is operably linked to the promoter of any of the aforementioned recombinant DNAs.
• the processed plant product comprises a feed, a meal, a flour, an extract, or a homogenate, wherein said feed, meal, flour, extract, or homogenate is obtained from at least one plant part.
• the processed plant product can be obtained from a plant part that is a stem, a leaf, a root, a flower, a tuber, or a seed.
• the processed product can comprise an extract that comprises a composition enriched for one or more protein(s), one or more monosaccharide(s), one or more disaccharide(s), one or more polysaccharides, or one or more fatty acid(s).
• processed plant products comprising a detectable amount of the protein encoded by the polynucleotide that is operably linked to the promoter of any of the aforementioned recombinant DNAs.
• the processed plant product comprises a feed, a meal, a flour, an extract, or a homogenate, wherein said feed, meal, flour, extract, or homogenate is obtained from at least one plant part.
• the processed plant product can be obtained from a plant part that is a stem, a leaf, a root, a flower, a tuber, or a seed.
• the processed product can comprise an extract that comprises a composition enriched for one or more protein(s), one or more monosaccharide(s), one or more disaccharide(s), one or more polysaccharides, or one or more fatty acid(s).
• a plant genomic DNA comprising a recombinant DNA molecule of any one of claims 1-14, or 15, wherein said recombinant DNA is stably integrated into a chromosome of said plant genomic DNA and wherein said recombinant DNA confers abiotic stress-tolerance to a plant comprising said chromosome.
• Figure 1 provides an alignment of the bacterial cold shock proteins forming the basis for the proteins of the present invention. Regions used in generating domain swap variants are indicated as Regl through Reg5.
• Figure 2 displays regions and specific targeted amino acid substitutions for variant generation using degenerate oligonucleotides.
• Figure 3 discloses a base vector for corn transformation.
• Figure 4 discloses a base vector for rice transformation.
• Figure 5 discloses a base vector for Arabidopsis transformation.
• Figure 6 discloses a base vector for soybean transformation.
• Figure 7 discloses a base vector for cotton transformation.
• the invention provides recombinant DNA derived from DNA encoding bacterial cold shock proteins where the recombinant DNA encodes a protein having one or more amino acid substitutions in the sequence of Bacillus subtilis CspB L2V (SEQ ID NO:1) or region swaps from among cold shock proteins from Escherichia coli (CspC (SEQ ID NO:4), CspD (SEQ ID NO:5), and CspG (SEQ ID NO:7)), Thermo anaerobacter tengcongensis (SEQ ID NO:3), Thermotoga maritime fSEQ ID NO:2), Agrobacterium tumefaciens (SEQ ID NO:6) and Bacillus subtilis (SEQ ID NO:1). DNA encoding these cold shock proteins are provided as SEQ ID NO:8 through SEQ ID NO: 14.
• bacterial cold shock protein(s) refers to any of: i) proteins that have at least 40% identity to any one of Bacillus subtilis CspB L2V (SEQ ID NO:1), Thermotoga maritime (SEQ ID NO:2), Thermoanaerobacter tengcongensis (SEQ ID NO:3), Escherichia coli CspC (SEQ ID NO:4), Escherichia coli CspD (SEQ ID NO:5), Agrobacterium tumefaciens (SEQ ID NO:6), ox Escherichia coli CspG (SEQ ID NO:7); and/or, ii) proteins comprising the conserved cold shock domain (Prosite motif PS00352; Bucher and Bairoch, (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology, Altman
• a bacterial cold shock protein is thus at least 40% identical, more preferably at least 50% identical, more preferably at least 60% identical, more preferably at least 70% identical, more preferably at least 80% identical, more preferably at least 90% identical, more preferably at least 95% identical, and most preferably at least 98% identical to any one of Bacillus subtilis CspB L2V (SEQ ID NO:1), Thermotoga maritime (SEQ ID NO:2), Thermoanaerobacter tengcongensis (SEQ ID NO:3), Escherichia coli CspC (SEQ ID NO:4), Escherichia coli CspD (SEQ ID NO:5), Agrobacterium tumefaciens (SEQ ID NO:6), or Escherichia coli CspG (SEQ ID NO:7).
• Bacillus subtilis CspB L2V SEQ ID NO:1
• Thermotoga maritime SEQ ID NO:2V
• enhanced abiotic stress tolerance characterizes a transgenic plant with enhanced tolerance to a high salt environment, heat exposure, drought exposure or water deficit environment or cold exposure as compared to a control plant.
• water deficit means a period when water available to a plant is not replenished at the rate at which it is consumed by the plant. A long period of water deficit is colloquially called drought. Lack of rain or irrigation may not produce immediate water stress if there is an available reservoir of ground water for the growth rate of plants.
• Plants grown in soil with ample groundwater can survive days without rain or irrigation without adverse affects on yield. Plants grown in dry soil are likely to suffer adverse affects with minimal periods of water deficit. Severe water deficit stress can cause wilt and plant death; moderate drought can cause reduced yield, stunted growth or retarded development. Plants can recover from some periods of water deficit stress without significantly affecting yield. However, water deficit stress at the time of pollination can have an irreversible effect in lowering yield. Thus, a useful period in the life cycle of corn for observing water deficit stress tolerance is the late vegetative stage of growth before tasseling. Water deficit stress tolerance is determined by comparison to control plants. For instance, plants of this invention can survive water deficit stress with a higher yield than control plants. In the laboratory and in field trials drought can be simulated by giving plants of this invention and control plants less water than is given to sufficiently-watered control plants and measuring differences in traits.
• a "control plant” may be a non-transgenic plant of the parental line used to generate a transgenic plant herein.
• a control plant may in some cases be a transgenic plant line that includes an empty vector or marker gene, but does not contain the recombinant polynucleotide of the present invention that is expressed in the transgenic plant being evaluated.
• a control plant in other cases is a transgenic plant expressing the gene with a constitutive promoter.
• a control plant is a plant of the same line or variety as the transgenic plant being tested, lacking the specific trait-conferring, recombinant DNA that characterizes the transgenic plant.
• Such a progenitor plant that lacks that specific trait-conferring recombinant DNA can be a natural, wild-type plant, an elite, non-transgenic plant, or a transgenic plant without the specific trait-conferring, recombinant DNA that characterizes the transgenic plant.
• the progenitor plant lacking the specific, trait-conferring recombinant DNA can be a sibling of a transgenic plant having the specific, trait-conferring recombinant DNA.
• Such a progenitor sibling plant may include other recombinant DNA
• the transgenic plants have enhanced yield, including increased yield under abiotic stress conditions and increased yield under non-stress conditions.
• Yield can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits.
• Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
• Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tons per acre, or kilo per hectare.
• corn yield may be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture.
• a bushel of corn is defined by law in the State of Iowa as 56 pounds by weight, a useful conversion factor for corn yield is: 100 bushels per acre is equivalent to 6.272 metric tons per hectare.
• Other measurements for yield are in common practice.
• a transgenic "plant cell” means a plant cell that is transformed with stably- integrated, non-natural, recombinant polynucleotides, e.g. by Agrobacterium-mediatQd transformation or by bombardment using microparticles coated with recombinant polynucleotides.
• a plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant polynucleotides in its chromosomal DNA, or seed or pollen derived from a progeny transgenic plant.
• transgenic plant or seed means one whose genome has been altered by the stable integration of recombinant polynucleotides in its chromosomal DNA, e.g. by transformation, by regeneration from a transformed plant from seed or propagule or by breeding with a transformed plant.
• transgenic plants include progeny plants of an original plant derived from a transformation process including progeny of breeding transgenic plants with wild type plants or other transgenic plants.
• the enhancement of a desired trait can be measured by comparing the trait property in a transgenic plant which has recombinant DNA conferring the trait to the trait level in a progenitor plant.
• abiotic stress tolerant transgenic plants include corn (maize), soybean, cotton, canola (rape), wheat, rice, alfalfa, sorghum, grasses such as switchgrass, vegetables and fruits.
• “Expressing a protein” means the function of a cell to transcribe recombinant DNA to mRNA and translate the mRNA to a protein.
• the recombinant DNA usually includes regulatory elements including 5 ' regulatory elements such as promoters, enhancers, and introns; other elements can include polyadenylation sites, transit peptide DNA, markers and other elements commonly used by those skilled in the art. Promoters can be modulated by proteins such as transcription factors and by intron or enhancer elements linked to the promoter. Promoters in recombinant polynucleotides can also be modulated by nearby promoters. [0042] "Recombinant DNA” means non-natural DNA, that has been prepared by modifying natural DNA or by combining segments of DNA, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques.
• Recombinant DNA for expressing a protein in a plant is typically provided as an expression cassette which has a promoter that is active in plant cells operably linked to DNA encoding a protein, e.g. a variant bacterial cold shock protein, linked to a 3' DNA element for providing a polyadenylation site and signal.
• Useful recombinant DNA also includes expression cassettes for expressing one or more proteins conferring herbicide tolerance and/or insect resistance.
• Useful promoters for expressing the variant cold shock proteins of the present invention in transgenic plant cells include constitutive promoters such as those from rice actin, rice GOS2 (SEQ ID NO:705), and CaMV35S.
• Promoters for use in the present invention may include a number of regulatory elements, such as enhancers, leaders and introns. Also of interest are chimeric promoters which include regulatory elements from different sources, such as the CaMV 35 S enhanced rice actin promoter provided herein as SEQ ID NO: 706. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in alternative embodiments of this invention to provide for expression of variant bacterial cold shock proteins in transgenic plant cells. [0043] Recombinant DNA constructs also generally include a 3' element that typically contains a polyadenylation signal and site.
• Well-known 3' elements include those from Agrobacterium tumefaciens genes such as nos 3 ', tml 3 ', tmr 3 ', tms 3 ', ocs 3 ', tr73 ', e.g., disclosed in U.S. 6,090,627.
• 3' elements from plant genes such as wheat (Triticum aestivum) heat shock protein 17 (Hspl7 3 '), a wheat ubiquitin gene, a wheat fructose- 1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene are disclosed in U.S.
• Constructs and vectors may also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
• a transit peptide for targeting of a gene target to a plant organelle particularly to a chloroplast, leucoplast or other plastid organelle.
• chloroplast transit peptides is disclosed in U.S. Patents 5,188,642 and 5,728,925.
• Patents 5,159,135 cotton; 5,824,877 (soybean); 5,591,616 (corn); and 6,384,301 (soybean), all of which are incorporated herein by reference.
• additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.
• Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment.
• Media refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism.
• Recipient cell targets include, but are not limited to, meristem cells, callus, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspores and the like.
• Cells capable of proliferating as callus are also recipient cells for genetic transformation.
• Practical transformation methods and materials for making transgenic plants of this invention, for example various media and recipient target cells, transformation of immature embryo cells and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Patents 6,194,636 and 6,232,526, which are incorporated herein by reference.
• transgenic plants can be harvested from fertile transgenic plants and be used to grow progeny generations of transformed plants of this invention including hybrid plants line for selection of plants having an enhanced trait.
• transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA.
• recombinant DNA can be introduced into first plant line that is amenable to transformation to produce a transgenic plant which can be crossed with a second plant line to intra gress the recombinant DNA into the second plant line.
• a transgenic plant with recombinant DNA providing an enhanced trait e.g.
• enhanced stress tolerance and/or yield can be crossed with a transgenic plant line having other recombinant DNA that confers another trait or traits, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers multiple traits.
• a transgenic plant line having other recombinant DNA that confers another trait or traits for example herbicide resistance or pest resistance
• progeny plants having recombinant DNA that confers multiple traits Typically, in breeding to combine traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base trait or traits is the female line.
• the progeny of this cross will segregate such that some of the plants will carry the DNA for traits present in both parents and some will carry DNA for the trait or traits from only one parent; such plants can be identified by markers associated with parental recombinant DNA, e.g.
• marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait.
• Progeny plants carrying DNA for traits from both parents can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line.
• Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a transgenic DNA construct into their genomes.
• Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers.
• Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA.
• Select marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (nptll), hygromycin B (aph IV) and gentamycin (aac3 and aacC ⁇ ) or resistance to herbicides such as glufosinate (bar or pat) and glyphosate (aroA or EPSPS). Examples of such selectable are illustrated in U.S. Patents 5,550,318; 5,633,435; 5,780,708 and 6,118,047.
• Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a ⁇ eto-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
• a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a ⁇ eto-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
• Transgenic plant cells that survive exposure to the selective agent or transgenic plant cells that have been scored positive in a screening assay are typically cultured in regeneration media and allowed to mature into plants.
• developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO 2 , and 25-250 micro einsteins m "2 s "1 of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue.
• Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn.
• the non-natural regenerated transgenic plants or progeny plants can be tested for the presence and expression of the recombinant DNA and selected for the presence of enhanced stress tolerance.
• Non-natural transgenic plants derived from the plant cells of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention.
• Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait.
• a selection method is designed to evaluate multiple transgenic plants (events) including the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events.
• Transgenic plants grown from transgenic seed provided herein demonstrate enhanced stress tolerance that contributes to increased yield.
• transgenic plant cells of this invention are identified by screening transformed progeny plants for enhanced stress tolerance and yield. For efficiency a screening program is designed to evaluate multiple transgenic plants preferably with a single copy of the recombinant DNA from two or more transgenic events.
• Transgenic plants having enhanced water use efficiency are identified by screening plants in an assay where water is withheld for period to induce stress followed by watering to revive the plants.
• a useful selection process for water defect tolerant transgenic corn plants imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle.
• the primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.
• Transgenic plants having enhanced cold tolerance are identified by screening plants in a cold germination assay and/or a cold tolerance field trial.
• a cold germination assay trays of transgenic and control seeds are placed in a growth chamber at 9.7 0 C for 24 days (no light). Seeds having higher germination rates as compared to the control are identified as having enhanced cold tolerance.
• plants with enhanced cold tolerance are identified from field planting at an earlier date than conventional Spring planting for the field location. For example, seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions preferably with multiple repetitions per treatment.
• Transgenic plants having enhanced yield are identified by screening using progeny of the transgenic plants over multiple locations with plants grown under optimal production management practices and maximum weed and pest control.
• a useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant.
• Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects.
• This example illustrates the preparation of recombinant DNA encoding proteins derived from bacterial cold shock proteins.
• Recombinant DNA is prepared which encodes proteins having single amino acid changes at amino acid positions Fl 5, F17, F27, H29 and F30 of Bs-CspB_L2V (SEQ ID NO:1) using degenerate 2'-OMe primers.
• DNA generated in this manner encodes proteins with the amino acid sequence of SEQ ID NO:53 through SEQ ID NO:57 and SEQ ID NO:458 through SEQ ID NO:578.
• Recombinant DNA is prepared which encodes proteins with Single amino acid changes at positions S31 and T40 of Bs-CspB_L2V (SEQ ID NO: 1). DNA generated in this manner encodes proteins with amino acid sequence of SEQ ID NO: 1.
• Recombinant DNA was prepared which encodes protein variants of Bs-CspB with two amino acid residues, N and N+2 (where N is any one of amino acids 2 - 65 of SEQ ID NO: 1), replaced with alanine residues. Where the amino acid at position N or N+2 is alanine, a serine was substituted for alanine.
• DNA generated in this manner encodes proteins with the amino acid sequence of SEQ ID NO:275 through SEQ ID NO:312.
• Other recombinant DNAs encoding protein variants of Bs-CspB with multiple alanine substitutions were made and encode proteins with the amino acid sequence of SEQ ID NO:270 through SEQ ID NO:274.
• Recombinant DNAs were also prepared by exchanging reciprocal DNA regions encoding the amino acid regions identified as "Reg 1"- "Reg 5" (See Figure 1) of the bacterial cold shock proteins of SEQ ID NOS: 1-7.
• DNA generated by region exchange encoded proteins having the amino acid sequence of SEQ ID NO: 16 through SEQ ID NO:23 and SEQ ID NO:313 through SEQ ID NO:427.
• the proteins encoded by the DNAs generated in this manner are designated as chimeric in the sequence listing.
• the name in the comments field for each protein indicates the donor region and the backbone sequence for the regions in the variant proteins.
• Chimeric Tm_Cspl_R2_Bs_CspB_bb refers to a chimeric variant bacterial cold shock protein sequence (SEQ ID NO: 17) having the R2 region of Thermotoga maritime Cspl exchanged into the backbone sequence of Bacillus subtilis CspB.
• SEQ ID NO: 17 a chimeric variant bacterial cold shock protein sequence having the R2 region of Thermotoga maritime Cspl exchanged into the backbone sequence of Bacillus subtilis CspB.
• Recombinant DNA encoding variant proteins of Bs-CspB having modifications in identified areas of sequence diversity and amino acid sequences that lie within the loop regions of Bs-CspB are generated using a degenerate oligonucleotide tail approach. The regions and specific targeted amino acid substitutions for variant generation are shown in Figure 2.
• DNAs produced as the result of this approach encode proteins having amino acid sequences of SEQ ID NO:15, SEQ ID NO:24 through SEQ ID NO:31, SEQ ID NO:58 through SEQ ID NO:269 and SEQ ID NO:579 through SEQ ID NO:704.
• Proteins encoded by the recombinant DNAs were expressed, purified and analyzed to determine their ability to complement the cold sensitivity of a quadruple E. co Ii mutant, BX04 (DE3) and to determine their ability to destabilize single stranded DNA secondary structure and bind to single stranded DNA.
• Constructs for expression of the proteins in transgenic plants are prepared using each of the recombinant DNAs operably linked to a promoter operable in plant cells.
• FIG. 3 A base vector useful for Agrobacterium-mediated transformation of corn, pMON74590, is shown in Figure 3.
• the vector provides an expression cassette for expression of DNA encoding proteins prepared in Example 1 under the control of an enhanced 35S/rice actin promoter (SEQ ID NO: 706).
• the transformation vector also contains an EPSPS gene as a selectable marker for resistance to glyphosate herbicide.
• the glyphosate resistance expression cassette comprises a rice actin 1 promoter, leader and intron operably linked to a DNA encoding a chloroplast transit peptide from an Arabidopsis thaliana EPSPS gene and DNA encoding an EPSPS from an A. tumefaciens gene (CP4) and a 3' element from an A. tumefaciens nopaline synthase gene.
• DNA having the sequence of SEQ ID NO: 34 through SEQ ID NO:52, encoding proteins prepared in Example 1, is cloned into pMON74590 and the resulting constructs are used for production of transgenic corn plants expressing variant bacterial cold shock proteins of SEQ ID NO:15 through SEQ ID NO:33.
• Plant expression constructs for rice transformation A base vector useful for Agrobacterium-mediatcd transformation of rice, pMONl 12481, is shown in Figure 4.
• the vector provides for enhanced protein expression under the control of a rice GOS2 gene promoter (SEQ ID NO:705).
• the transformation vector also contains an EPSPS gene as a selectable marker for resistance to glyphosate herbicide.
• the glyphosate resistance expression cassette comprises a rice actin 1 promoter, leader and intron operably linked to a DNA encoding a chloroplast transit peptide from an Arabidopsis thaliana EPSPS gene and DNA encoding an EPSPS from an A.
• CP4 tumefaciens gene
• DNA having the sequence of SEQ ID NO: 34 through SEQ ID NO:52, encoding proteins prepared in Example 1, is cloned into pMONl 12481 and the resulting constructs are used for production of transgenic corn plants expressing variant bacterial cold shock proteins of SEQ ID NO:15 through SEQ ID NO:33.
• a base vector useful for Agrobacterium-mediated transformation of Arabidopsis is shown in Figure 5.
• the vector provides for enhanced protein expression under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. patent 5,359,142).
• the transformation vector also contain an EPSPS gene as a selectable marker for resistance to glyphosate herbicide.
• the glyphosate resistance expression cassette comprises a rice actin 1 promoter, leader and intron operably linked to a DNA encoding a chloroplast transit peptide from an Arabidopsis thaliana EPSPS gene and DNA encoding an EPSPS from an A. tumefaciens gene (CP4) and a 3' element from an A.
• DNA having the sequence of SEQ ID NO: 34 through SEQ ID NO:52, encoding proteins prepared in Example 1, is cloned into pMON 100407 and the resulting constructs are used for production of transgenic Arabidopsis plants expressing variant bacterial cold shock proteins of SEQ ID NO:15 through SEQ ID NO:33.
• Additional constructs are generated using recombinant DNA encoding variant bacterial cold shock proteins of SEQ ID NO:258, SEQ ID NO:268, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:334, SEQ ID NO:343, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:367, SEQ ID NO:377, SEQ ID NO:380, SEQ ID NO:381, SEQ ID NO:385, SEQ ID NO:391, SEQ ID NO:397, SEQ ID NO:403, SEQ ID NO:449 and SEQ ID NO:622.
• the transformation of Arabidopsis plants is carried out using a vacuum infiltration method (Bechtold, e.g., Methods MoI. Biol.
• Plant expression constructs for soybean transformation [0071] A base vector useful for Agrobacterium-mediatQd transformation of soybean, pMON82053, is shown in Figure 6. The vector provides for enhanced protein expression under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. patent 5,359,142). The transformation vector also contain an EPSPS gene as a selectable marker for resistance to glyphosate herbicide.
• the glyphosate resistance expression cassette comprises a rice actin 1 promoter, leader and intron operably linked to a DNA encoding a chloroplast transit peptide from an Arabidopsis thaliana EPSPS gene and DNA encoding an EPSPS from an A. tumefaciens gene (CP4) and a 3' element from an A. tumefaciens nopaline synthase gene.
• Recombinant DNA for expression of variant bacterial cold shock proteins is cloned into pMON82053 and the resulting constructs are used for transformation of transgenic soybean plants expressing variant bacterial cold shock proteins.
• a base vector useful for Agrobacterium-mediatQd transformation of cotton is shown in Figure 7.
• the vector provides for enhanced protein expression under the control of an enhanced CaMV 35S promoter.
• the transformation vectors also contain an nptll gene as a selectable marker for resistance to antibiotics such as kanamycin.
• Recombinant DNA for expression of variant bacterial cold shock proteins is cloned into pMON99053 and the resulting constructs are used for transformation of transgenic cotton plants expressing variant bacterial cold shock proteins.
• This example illustrates the production of multiple transgenic events of transgenic corn plants expressing each of the recombinant DNAs prepared in Example 1 using the vectors prepared in Example 2.
• Transgenic corn plants are made from cells transformed by Agrobacterium mediated transformation using DNA constructs prepared in Example 2.
• Transgenic plants having recombinant DNA stably inserted in the chromosome and expressing proteins having the amino acid sequences of SEQ ID NO:15 through SEQ ID NO:33, are evaluated for stress tolerance, including yield under water deficit stress. Events of these transgenic plants are identified that have increased tolerance to abiotic stress as compared to control plants. Transgenic seed is collected from the identified plants.
• Transgenic rice plants are prepared by Agrobacterium mediated transformation using DNA constructs described in Example 2.
• Transgenic plants having recombinant DNA stably inserted in the chromosome and expressing a protein prepared in Example 1 are identified and evaluated for stress tolerance, including yield under water deficit stress. Events of these transgenic plants are identified that have increased tolerance to abiotic stress as compared to control plants. Transgenic seed is collected from the identified plants.
• Example 5
• Transgenic cotton plants are prepared by Agrobacterium mediated transformation using DNA constructs described in Example 2.
• Transgenic plants having recombinant DNA stably inserted in the chromosome and expressing a protein prepared in Example 1 are identified and evaluated for stress tolerance, including yield under water deficit stress. Events of these transgenic plants are identified that have increased tolerance to abiotic stress as compared to control plants. Transgenic seed is collected from the identified plants.
• Transgenic soybean plants are prepared by Agrobacterium mediated transformation using DNA constructs described in Example 2.
• Transgenic plants having recombinant DNA stably inserted in the chromosome and expressing a protein prepared in Example 1 are identified and evaluated for stress tolerance, including yield under water deficit stress. Events of these transgenic plants are identified that have increased tolerance to abiotic stress as compared to control plants. Transgenic seed is collected from the identified plants.
• Transgenic alfalfa, canola, switchgrass and sugarcane plants comprising DNA constructs stably inserted in the chromosome and expressing a protein prepared in Example 1 are prepared and evaluated for stress tolerance, including yield under water deficit stress. Events of these transgenic plants are identified that have increased tolerance to abiotic stress as compared to control plants. Transgenic seed is collected from the identified plants.
• This example illustrates the various stress tolerance properties of heterozygous hybrid corn plants expressing a protein with a cold shock domain.
• Corn plants were screened for enhanced cold stress tolerance by measuring germination and/or early seedling growth at cold temperature, water deficit stress tolerance in a greenhouse "drought" screen, and water deficit tolerance in a random field screen in which plants from randomly planted seed were subjected to water deficit allowing an investigator to observe and select plants with positive water deficit tolerance.
• Table 1 showing the number of transgenic events tested for recombinant DNA expressing the various proteins and whether events were identified as showing water deficit or cold stress tolerance.

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